Thanks to all. Mapmask works. Yes the order to change to is ZXY. Map from coefficients indeed looks like the directly loaded map, jus the scale is different (I supplied no reference PDB)
The remaining issue is - a pain to automate. I tried Refmac- there is a mention of an sfall mode and I tried to input the map and a reference HKL .. In that case, refmac simply stops after reading the map. If I add a XYZIN to scale the map, I get a mtz but not from the map, which is never read. I am not even sure – this is from the EM part in the instructions – if this is intended to work in this fashion. Has somebody tried that successfully with an Xray map? Many thanks again, BR From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Alejandro Buschiazzo Sent: Thursday, May 14, 2020 15:10 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Using SFall for map conversion Oh…maybe I suggested the wrong order then (Y X Z - for SG 20) ? …I do realize YXZ is not an XYZ cyclic permutation (whereas ZXY is)…I dug it from an old script of mine, so now rechecked the FFT doc …but yes, FFT says that Y X Z is the std axis ordering for SGs higher-than 18…I’m probably missing something silly here (any clue James?) Best, ale On May 14, 2020, at 6:45 PM, James Holton <jmhol...@lbl.gov <mailto:jmhol...@lbl.gov> > wrote: Use mapmask first: echo axis Z X Y |\ mapmask mapin1 old.map mapout new.map For reasons I'm sure made sense at one time, sfall does not seem to know how to automatically re-order the map axes. Also, it is generally a good idea to expand to P1 first, and use "SFSG 1" in sfall. There are still some "gotcha" space groups in the SFALL code for density near cell edges. I can't remember which ones now because years ago I started using SFSG 1 and the problem went away. -James Holton MAD Scientist On 5/14/2020 1:44 PM, Bernhard Rupp wrote: Hi Fellows, I am failing on conversion of a ccp4 map to mtz using Sfall I provide as a scale reference a mtz with FP SIGFP and R free All cell constants and SG 20 and map headers seem to agree. But I receive following warning: *** WARNING - your map spacegroup is different to the program default one *** and later >>>>>> CCP4 library signal library_ <file:///Cannot> file:Cannot open file >>>>>> (Warning) raised in tmpfile() failed, opening normal file instead. <<<<<< INPUT X USED AS X INPUT Y USED AS Z INPUT Z USED AS Y Which then leads to the imho - given above- justified complaint: Check map header agrees with fixed requirements for SFcalc for this spacegroup. Check Nxyz 180 200 120 180 200 120 Check map header agrees with fixed requirements for SFcalc for this spacegroup. Check Iuvw 3 2 1 3 1 2 <B><FONT COLOR="#FF0000"> SFALL: **** Fatal disagreement between input info and map header How do I fix this ? In principle all the information is there to do the job… Many thx, BR ------------------------------------------------------ Bernhard Rupp Crystallographiae Vindicis Militum Ordo <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/ <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org +1 925 209 7429 +43 676 571 0536 ------------------------------------------------------ Many plausible ideas vanish at the presence of thought ------------------------------------------------------ _____ To unsubscribe from the CCP4BB list, click the following link: <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 _____ To unsubscribe from the CCP4BB list, click the following link: <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 _____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
